ArticlePLoS genetics2016
A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Aging: a possible road toward gut microbiota pathoadaptation.Gut microbes · 2025Article
- Evolutionary adaptation of probiotics in the gut: selection pressures, optimization strategies, and regulatory challenges.NPJ biofilms and microbiomes · 2025Review
- Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut.Nature microbiology · 2024Article
- Massively parallel single-cell sequencing of diverse microbial populations.Nature methods · 2024Article
- Mutational hotspots lead to robust but suboptimal adaptive outcomes in certain environments.Microbiology (Reading, England) · 2023Article
- Predicting the effect of mutations to investigate recent events of selection across 60,472Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Shared Evolutionary Path in Social Microbiomes.Molecular biology and evolution · 2023Article
- Article
- Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations.Nature communications · 2022Article
- Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements.Cell host & microbe · 2022Article
- Article
- Evolved bacterial resistance against fluoropyrimidines can lower chemotherapy impact in theeLife · 2020Article
- Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut.Nature ecology & evolution · 2020Article
- Evolutionary stalling and a limit on the power of natural selection to improve a cellular module.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Horizontal gene transfer overrides mutation inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- "I will survive": A tale of bacteriophage-bacteria coevolution in the gut.Gut microbes · 2019Article
- Inactivation of a Mismatch-Repair System Diversifies Genotypic Landscape ofFrontiers in microbiology · 2019Article
- Article
- Recurrent Reverse Evolution Maintains Polymorphism after Strong Bottlenecks in Commensal Gut Bacteria.Molecular biology and evolution · 2017Article
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The relative role of drift versus selection underlying the evolution of bacterial species within the gut microbiota remains poorly understood. The large sizes of bacterial populations in this environment suggest that even adaptive mutations with weak effects, thought to be the most frequently occurring, could substantially contribute to a rapid pace of evolutionary change in the gut. We followed the emergence of intra-species diversity in a commensal Escherichia coli strain that previously acquired an adaptive mutation with strong effect during one week of colonization of the mouse gut. Following this first step, which consisted of inactivating a metabolic operon, one third of the subsequent adaptive mutations were found to have a selective effect as high as the first. Nevertheless, the order of the adaptive steps was strongly affected by a mutational hotspot with an exceptionally high mutation rate of 10-5. The pattern of polymorphism emerging in the populations evolving within different hosts was characterized by periodic selection, which reduced diversity, but also frequency-dependent selection, actively maintaining genetic diversity. Furthermore, the continuous emergence of similar phenotypes due to distinct mutations, known as clonal interference, was pervasive. Evolutionary change within the gut is therefore highly repeatable within and across hosts, with adaptive mutations of selection coefficients as strong as 12% accumulating without strong constraints on genetic background. In vivo competitive assays showed that one of the second steps (focA) exhibited positive epistasis with the first, while another (dcuB) exhibited negative epistasis. The data shows that strong effect adaptive mutations continuously recur in gut commensal bacterial species.
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